The program that I like to use for this is PyMOL. It works great but I have to admit that I haven't tried any other comparable programs. First you open the molecule file that you just produced. On the right side its name appears. Go there and click zoom. Change the the preset to "ball and stick". Change the color to how you want your carbons and then go for color by element. The carbons will stay the way you had them.
I usually like a 1440x900 picture because that fits my screen. With typing "viewport 960,600" the window is on scale and I can still see everything. I rotate and zoom the molecule until it looks nice. Then I type "ray 1440,900" to raytrace the picture. If I like it I save it. If I don't I can change some of the settings.
PyMOL related links are: the official manual - it definitely makes sense to work through that once. PyMOL scripts - I use a modified pymolrc file to set the background color and the viewport. PyMOLWiki - I haven't really found much information I could use there.
POV-Ray is a raytracing program that can be used in connection with ArgusLab. ArgusLab has an option for exporting into the POV-Ray format. I don't think it is as convenient to use as PyMOL. I don't like the pictures as much either. It probably has much more options but PyMOL has a few very nice looking presets.
The problem is that the browser crashes if two applets are opened like this on same page. Maybe the problem is that "jmolInitialize" is carried out twice. I might be able to solve the problem if I put that into the header, too. But I am not sure about that and who needs so many moving things anyway. I can't put an applet here for that reason but you can look at BINAP.